Mutations in the gene coding for Escherichia coli DNA topoisomerase I affect transcription and transposition

Mechanism of inhibition of mammalian DNA topoisomerase I by heparin

We have previously shown that heparin is a potent inhibitor of a mammalian DNA topoisomerase I. We have now investigated the mechanism of its inhibition. This was carried out first by scrutinizing the structural features of heparin molecules responsible for the inhibition. Commercial heparin preparation was fractionated by antithrombin III-Sepharose into non-adsorbed, low-affinity and high-affinity fractions, of which only the high-affinity fraction of heparin is known to contain a specific oligosaccharide sequence responsible for the binding to antithrombin III. These fractions all exhibited essentially similar inhibitory activities. Furthermore, when chemically sulphated to an extent comparable with or higher than heparin, otherwise inactive glycosaminoglycans such as heparan sulphate, chondroitin 4-sulphate, dermatan sulphate and neutral polysaccharides such as dextran and amylose were converted into potent inhibitors. Sulphated dermatan sulphate, one of the model compounds, was further shown to bind competitively to the same sites on the enzyme as heparin. These observations strongly suggested that topoisomerase inhibition by heparin is attributable primarily, if not entirely, to the highly sulphated polyanionic nature of the molecules. In a second series of experiments we examined whether heparin inhibits only one or both of the topoisomerase reactions, i.e. nicking and re-joining. It was demonstrated that both reactions were inhibited by heparin, but the nicking reaction was more severely affected than was the re-joining reaction.

Inhibition of topoisomerase I by antibodies in sera from scleroderma patients

Purified type I topoisomerase from calf thymus as well as nuclear and cytoplasmic extracts from EGF-stimulated human and mouse fibroblasts in cell culture efficiently convert supercoiled plasmid DNA to the relaxed form. The purified IgG fraction from the sera of Japanese patients with the rheumatic disease scleroderma were shown to inhibit this relaxation activity. Thus, these patients likely produce autoantibodies to topoisomerase I. In addition, the human, bovine and murine enzymes share antigenic determinants recognized by the antisera.

The pyridine nucleotide cycle of Salmonella typhimurium: genetic characterization of the pncXA operon

A series of Mud1 and Tn10 insertions were identified in the pncA chromosome region of Salmonella typhimurium which is responsible for the production of nicotinamide deamidase. Both pncA (resulting in no nicotinamide deamidase activity) and pncX (resulting in lowered nicotinamide deamidase activity) insertions were constructed. In addition, mutants which could utilize nicotinamide as a sole source of nitrogen were isolated. These mutants, designated pncH, hyperproduce nicotinamide deamidase. Genetic studies utilizing pncX--lacZ and pncA--lacZ operon fusions indicate that pncX::Tn10 insertions reduce transcription of pncA--lac while pncH mutations increase the expression of both pncA--lacZ and pncX-lacZ. The gene order was determined as purB--pncA--pncX--gdh with transcription of both pncA and pncX occurring in the counterclockwise direction. Merodiploid studies suggest a model whereby pncX and pncA form an operon with the major promoter occurring upstream from pncX. A second, weaker promoter for pncA must be situated between pncX and pncA. The pncH mutations appear to occur in the pncX promoter (pncXp) increasing promoter activity.

Topoisomerase I mutants: the gene on pBR322 that encodes resistance to tetracycline affects plasmid DNA supercoiling

Plasmid pBR322 DNA isolated from topoisomerase I mutants of Escherichia coli and Salmonella typhimurium exhibits a distinctive supercoiling distribution characterized by an extremely heterogeneous distribution of linking numbers that contains highly negatively supercoiled topoisomers. Analysis of the supercoiling distributions of deletion and insertion derivatives of pBR322 shows that the presence of the gene on pBR322 encoding resistance to tetracycline is responsible for the unusual supercoiling distribution. Both an intact promoter and a portion of the remainder of the gene, but not the gene product, are required. However, no particular section of the gene outside the promoter appears to be necessary; only the size of the section remaining appears to be important. These observations suggest that transcription of this gene may be responsible for its effect on DNA supercoiling.

Effects of DNA gyrase inhibitors in Escherichia coli topoisomerase I mutants

Relaxation of titratable supercoils in bacterial nucleoids was measured following treatment of topA mutants with coumermycin or oxolinic acid, inhibitors of DNA gyrase. Relaxation occurred after treatment of the mutants with either inhibitor. We detected no significant difference in relaxation between topA- and topA+ strains treated with coumermycin. This finding, together with previous observations, supports the idea that relaxation caused by coumermycin probably arises from the relaxing activity of gyrase itself. The source of DNA relaxation caused by oxolinic acid was not identified. Nucleoid supercoiling can be increased by adding oxolinic acid to a strain that carries three topoisomerase mutations: delta topA, gyrB225, and gyrA (Nalr) (S. H. Manes, G. J. Pruss, and K. Drlica, J. Bacteriol. 155:420-423, 1983). We found that this increase in supercoiling requires partial sensitivity to the drug and at the delta topA and gyrA mutations. Full resistance to oxolinic acid in the presence of the delta topA, gyrB225, and gyrA mutations was conferred by an additional mutation that maps at or near gyrB.

The Escherichia coli supX locus is topA, the structural gene for DNA topoisomerase I

Mutations in the supX locus, which result in the absence of DNA topoisomerase I enzyme activity in both Salmonella typhimurium and Escherichia coli, are all selected as suppressors of the leu-500 promoter mutation in S. typhimurium. To determine whether the supX locus is the structural gene topA for the DNA topoisomerase I enzyme or is a positive-acting regulator/activator gene for a nearby topA structural gene, nonsense mutations were selected in the E. coli supX gene carried on an F' episome in S. typhimurium cells. The cysB-topA region of the episomes with nonsense-mutant supX alleles were then cloned onto plasmid pBR322 and transformed into E. coli cells lacking a chromosomal supX gene. Three such E. coli strains, each carrying cloned DNA from episomes with different nonsense-mutant supX alleles, all lacked DNA topoisomerase I activity but expressed antigenic determinants specific to the enzyme; control cells lacked both enzyme activity and antigenic determinants. Maxicell studies of plasmid-coded proteins demonstrated the absence of the DNA topoisomerase I protein (100 kDa) in the three strains but the appearance of a new smaller peptide in each (36, 47, and 64 kDa). These new peptides must represent fragments of the enzyme resulting from translation termination at the supX nonsense codons and confirm the interpretation that the supX gene is topA, the structural gene for DNA topoisomerase I.

Regulation of the Escherichia coli DNA topoisomerase I gene by DNA supercoiling

The transcriptional control region of THE E. coli DNA topoisomerase I (topA) gene has been fused to the galactokinase (galK) gene coding region in a recombinant plasmid. In vivo synthesis of the galactokinase produced from such a plasmid has been measured and found to be reduced when mutations in the genes coding for DNA gyrase subunits are introduced into the cell or when gyrase inhibitors are present. In vitro transcription-translation of the galactokinase gene product confirms that a supercoiled DNA template is required for efficient transcription from the topA gene promoter. These results indicate that the amount of DNA topoisomerase I activity in E. coli is regulated by the extent of DNA supercoiling and can contribute to the overall modulation of DNA superhelicity and the expression of other genes.

Cloning, characterization, and sequence of the yeast DNA topoisomerase I gene

The structural gene for yeast DNA topoisomerase I (TOP1) has been cloned from two yeast genomic plasmid banks. Integration of a plasmid carrying the gene into the chromosome and subsequent genetic mapping shows that TOP1 is identical to the gene previously called MAK1. Seven top1 (mak1) mutants including gene disruptions are viable, demonstrating that DNA topoisomerase I is not essential for viability in yeast. A 3787-base-pair DNA fragment including the gene has been sequenced. The protein predicted from the DNA sequence has 769 amino acids and a molecular weight of 90,020.

Genetic analysis of mutations that compensate for loss of Escherichia coli DNA topoisomerase I

A transposon Tn10 insertion in topA, the structural gene of Escherichia coli DNA topoisomerase I, behaves as an excluded marker in genetic crosses with many strains of E. coli. However, derivative strains that accept this mutant topA allele are readily selected. We show that many of these topA mutant strains contain additional mutations that compensate for the loss of DNA topoisomerase I. Genetic methods for mapping and manipulating such compensatory mutations are described. These methods include a plate-mating test for the ability of strains to accept a topA::Tn10 allele and a powerful indirect selection for transferring compensatory mutations from male strains into non-compensatory female strains. One collection of spontaneous compensatory mutants is analyzed in detail and is shown to include compensatory mutations at three distinct loci: gyrA and gyrB, the genes that encode the subunits of DNA gyrase, and a previously unidentified locus near tolC. Mutations at this third locus, referred to as toc (topoisomerase one compensatory) mutations, do not behave as point mutations in transductional crosses and do not result in lowered DNA gyrase activity. These results show that wild-type strains of E. coli require DNA topoisomerase I, and at least one class of compensatory mutations can relieve this requirement by a mechanism other than reduction of DNA gyrase activity.

Eukaryotic type I topoisomerase is enriched in the nucleolus and catalytically active on ribosomal DNA

The distribution of eukaryotic DNA topoisomerase I in the cell has been analyzed at four levels: (i) at the level of the nuclear matrix; (ii) at the cytological level by immunofluorescence of whole cells; (iii) at the electron microscopic level using the protein A/colloidal gold technique; and (iv) at the level of DNA to identify in situ the sequence upon which topoisomerase I is catalytically active. Although topoisomerase I is clearly distributed non-randomly in the nucleus, the unique distribution of the enzyme is not related to the nuclear matrix. The data support the conclusion that topoisomerase I is heavily concentrated in the nucleolus of the cell; furthermore, particular regions within the nucleolus are depleted of topoisomerase. A technique has been developed which allows isolation and analysis of the cellular DNA sequences covalently attached to topoisomerase. Ribosomal DNA sequences are at least 20-fold enriched in topoisomerase/DNA complexes isolated directly from a chromosomal setting, relative to total DNA. This is the first direct evidence that topoisomerase I is catalytically active on ribosomal DNA in vivo.

Mechanisms determining aerobic or anaerobic growth in the facultative anaerobe Salmonella typhimurium

We isolated mutant strains of the facultative anaerobe Salmonella typhimurium that grow either aerobically or anaerobically. Strict anaerobic mutants contained a defective DNA topoisomerase I gene (topI), while strict aerobic mutants contained a defective DNA gyrase subunit A gene (gyrA, also nalA). Topoisomerase I activity was detected in cell-free extracts of strict aerobic mutants but not of strict anaerobic mutant strains, whereas gyrase activity was detected in extracts of strict anaerobic mutants but not of strict aerobic mutants. Furthermore, extracts of wild-type cells, cultured under vigorous aerobic condition, contain topoisomerase I activity but no significant gyrase activity. In contrast, the extracts of anaerobically cultured wild-type cells contain gyrase activity but no significant topoisomerase I activity. Sucrose gradient centrifugation with ethidium bromide showed that chromosomal DNA in strict aerobic mutants and aerobically grown wild-type cells was relaxed, while the chromosomal DNA of strict anaerobic mutants and anaerobically grown wild-type cells was more supercoiled. Aerobic cultures of wild type and strict aerobic mutants produced both superoxide dismutase and catalase, whereas anaerobic cultures of wild type and strict anaerobic mutants did not. These results lead us to conclude that activity of topoisomerase I, associated with relaxation of chromosomal DNA, is necessary for expression of genes required for aerobic growth, whereas activity of gyrase, associated with supercoiling of chromosomal DNA, is necessary for expression of genes required for anaerobic growth.

Involvement of DNA superhelicity in minichromosome maintenance in Escherichia coli

Evidence is presented that Escherichia coli minichromosomes are harbored at superhelical densities which are lower than those measured for other E. coli plasmids but are comparable to that of the chromosome. When introduced into gyrB decreased-supercoiling mutants, minichromosomes were much more unstable than in strains with normal or increased supercoiling properties; in fact, certain minichromosome derivatives could not be introduced into top gyrB decreased-supercoiling mutants. These observations were unique to minichromosomes, since the maintenance of plasmids which did not replicate from oriC was not altered in these mutants. Analyses of minichromosomes of identical sizes but with different restriction fragment orientations suggested that supercoiling-dependent alterations in promoter-terminator functions, as well as direct effects of supercoiling on replication, may play a role in the observed minichromosome instability.

Isolation and characterization of antisuppressor mutations in Escherichia coli

Nonsense mutations in lacI have been shown to be useful as indicators of the efficiency of nonsense suppression. From strains containing supE and a lacI nonsense mutation, selection for LacI- mutants has resulted in the isolation of four antisuppressor mutations. Tn10 insertions linked to these mutations were isolated and used to group the four mutations into three loci. The asuA1 and asuA2 mutations are linked to trp, reduce suppression by supE approximately twofold, and affect a variety of suppressors. The asuB3 mutation was mapped by P1 cotransduction to rpsL but does not confer resistance to streptomycin. The asuC4 mutation reduced suppression by supE by 95% and was shown biochemically to result in the loss of two pseudouridine modifications from the 3' side of the anticodon stem and loop of tRNA2Gln. This mutation is linked to purF, suggesting that it is a new allele of hisT.

Escherichia coli strains containing mutations in the structural gene for topoisomerase I are recombination deficient

Mutations in the gene encoding topoisomerase I of Escherichia coli were tested for their effect on plasmid recombination. Recombination was decreased 1,000-fold at 30 and 37 degrees C and occurred at approximately wild-type frequencies at 42 degrees C. The suppression of topA mutations at 42 degrees C did not appear to be a result of increased topoisomerase I activity at 42 degrees C.

Relaxation of supercoiled plasmid DNA by oxidative stresses in Escherichia coli

The relaxation of plasmid DNA was observed after the visible light irradiation of Escherichia coli AB1157 harboring plasmid pBR322 or some other plasmids in the presence of a photosensitizing dye, such as toluidine blue or acridine orange, and molecular oxygen. Treatment of the cells with hydroperoxides, such as tert-butyl hydroperoxide, cumene hydroperoxide, and hydrogen peroxide, also caused the plasmid DNA relaxation in vivo. Relaxation was not observed in these treatments of purified pBR322 DNA in vitro. Plasmid DNA relaxation was also detected after near-UV irradiation. Far-UV irradiation did not induce such relaxation.

A protein kinase activity tightly associated with Drosophila type II DNA topoisomerase

A protein kinase activity has been identified that is tightly associated with the purified Drosophila type II DNA topoisomerase. The kinase and topoisomerase activities are not separated when the enzyme is subjected to analytical chromatography (phosphocellulose, single-strand DNA agarose, and Sephacryl S-300) and analytical glycerol gradient sedimentation. These two activities are also inactivated to the same extent by either heat or N-ethylmaleimide treatment. The evidence, however, does not rule out the possibility that the kinase activity resides in a polypeptide other than the topoisomerase polypeptide. The topoisomerase-associated protein kinase activity is not stimulated by Ca2+ or cyclic nucleotides. It shows a broad substrate range, including the DNA topoisomerase itself, casein, phosvitin, and histones. Phosphoamino acid analysis identified phosphoserine and phosphothreonine in polypeptides modified by the topoisomerase-associated protein kinase. No similar activity has been identified previously in Drosophila melanogaster.

Topological repression of gene activity by a transposable element

The ebgA (evolved beta-galactosidase) gene of Escherichia coli was isolated as part of a 9.6-kilobase (kb) sequence cloned into plasmid pBR322. The position of the ebgA gene within that 9.6-kilobase sequence was identified by insertional inactivation by means of the transposon gamma-delta. In addition to the gamma-delta insertions that inactivate ebgA by disrupting the coding sequence, seven additional gamma-delta insertions reduce expression of the gene by a factor of greater than 200 by insertions elsewhere into the replicon. One of these insertions is into the pBR322 sequence itself. This action at a distance to reduce expression requires that gamma-delta is cis with respect to the ebgA gene. The effect is independent of the orientation or position of gamma-delta within the replicon, but it does depend both upon the orientation of the ebgA-bearing sequence within the replicon and upon the total size of the replicon. Transcription readthrough (promoter occlusion) does not explain this phenomenon, and we suggest that the presence of gamma-delta may alter the local supercoiling in the region of the ebgA promoter in such a way as to inhibit transcription. This repression by a transposable element appears to represent a novel mechanism for altering gene expression.

Native supercoiling of DNA: the effects of DNA gyrase and omega protein in E. coli

This study deals with the effects of a temperature-sensitive (ts) mutation at the gene encoding the DNA gyrase B subunit (gyrBts) and a deletion of the top gene encoding the omega protein upon the superhelical density of the pAO3 plasmid in E. coli cells. The alteration of the DNA gyrase B subunit is shown to lead to a partial relaxation of DNA. On the other hand, the lack of omega protein due to the top gene deletion leads to an abnormally high degree of DNA supercoiling. In a double gyrBts delta top mutant the DNA supercoiling is greater than native at the permissive temperature, while under nonpermissive conditions a partial relaxation is observed. However, the pattern of DNA relaxation in the latter case is quite different from that in a single gyrBts mutant. The conclusion is that the native supercoiling of DNA in the cell is maintained through the counter-activities of DNA gyrase and the omega protein.

DNA sequence and transcription of the region upstream of the E. coli gyrB gene

We have determined the sequence of a 1498 base-pair region in E. coli that extends from within dnaN through recF and into the gyrB gene. An open reading frame of 1071 base pairs has been identified with the recF structural gene. By S1 mapping, we have located a transcription start point 31 base pairs upstream of gyrB. The amount of this transcript is much greater in cells that have been treated with novobiocin, a treatment which is known to induce greater synthesis of DNA gyrase.

Transition of deletion mutants of the composite resistance plasmid NR1 in Escherichia coli and Salmonella typhimurium

Derivatives of the composite R plasmid NR1 from which a portion of the resistance determinants (r-determinants) component had been deleted were found to undergo amplification of the remaining r-determinants region in Escherichia coli and Salmonella typhimurium. The wild-type NR1 plasmid does not amplify in these genera, although all of these plasmids undergo amplification in Proteus mirabilis. The deletion mutants retained the mercuric ion resistance operon (mer) but conferred a much lower level of sulfonamide resistance than NR1. The remaining r-determinants region, which is bounded by direct repeats of the insertion element IS1, formed multiple tandem duplications in E. coli, S. typhimurium, and P. mirabilis after subculturing the host cells in medium containing high concentrations of sulfonamide. Gene amplification was characterized by restriction endonuclease analysis, analytical buoyant density centrifugation, DNA-DNA hybridization, and sedimentation in sucrose gradients. The tandem repeats remained attached to the resistance transfer factor component of the plasmid in at least part of the plasmid population; autonomous tandem repeats of r-determinants were probably also present. Amplification did not occur in host recA mutants. Amplified strains subcultured in drug-free medium lost the amplified r-determinants. By using a strain temperature sensitive for the recA gene, it was possible to obtain gene amplification at the permissive temperature. Loss of r-determinants took place at the permissive temperature, but not at the nonpermissive temperature. The termini of the deletions of several independent mutants which conferred low sulfonamide resistance were found to be located within the adjacent streptomycin-spectinomycin resistance gene.

Regulation of bacterial DNA supercoiling: plasmid linking numbers vary with growth temperature

The level of DNA supercoiling can be altered either by breaking-rejoining reactions that change the DNA linking number or by environmental changes that alter the helical pitch of DNA. In vitro, temperature changes alter helical pitch and, thus, supercoiling. We find that plasmids isolated from bacteria grown at different temperatures exhibit differences in DNA linking numbers. The differences in plasmid linking numbers offset the effect temperature is expected to have on supercoiling. These results are consistent with the hypothesis that fine control of DNA topology in bacterial cells is brought about by changes in linking number to maintain a constant value for supercoiling.

Reverse gyrase--a topoisomerase which introduces positive superhelical turns into DNA

An enzymatic activity which converts closed circular DNA into a positively supercoiled form is present in cellular extracts of Sulfolobus, an acidothermophilic archaebacterium. This novel enzyme is a type II DNA topoisomerase and is active only at temperatures greater than 55 degrees C, in the presence of ATP and Mg2+.

Genetic inactivation of topoisomerase I suppresses a defect in initiation of chromosome replication in Escherichia coli

A strain of Escherichia coli K12 harboring simultaneously the temperature-sensitive dnaA46 mutation and a deletion of the trp-topA-cysB region plates with the same full efficiency at 30 degrees C and 42 degrees C. We have analyzed the possible involvement of the gene coding for topoisomerase I, topA, in this suppression phenomenon. The Ts phenotype was retrieved upon introduction of a plasmid-borne DNA fragment including an active topA gene into this strain, but not upon introduction of the same fragment harboring a topA::Tn1000 insertion. Replication seems to remain DnaA-dependent in the delta (topA) strain, however, since we have been unable to introduce a dnaA::Tn10 allele. We propose either that the dnaA46 gene product is overproduced and compensates for its thermal inactivation, or that initiation at oriC demands less DnaA protein in the absence of topoisomerase I.

Promoter mutation causing catabolite repression of the Salmonella typhimurium leucine operon

Two mutations that affect expression of the Salmonella typhimurium leu operon were investigated. leu operon DNA from these mutant strains was cloned, and nucleotide sequences of the leu control regions were determined. leu-500, which eliminates expression of all four leu genes simultaneously, is a point mutation in the -10 region of the leu promoter. leu-2012 is a point mutation within the -35 region of the leu promoter. leu-2012 suppressed leucine auxotrophy caused by leu-500 only when the medium contained a carbon source that does not cause catabolite repression. A cya mutation (adenylate cyclase deficiency) introduced into the leu-500 leu-2012 strain caused leu enzymes to be made only if cAMP was supplied exogenously. A leu-500 leu-2012 strain containing a crp mutation (cAMP receptor protein deficiency), on the other hand, could not make leu enzymes even in the presence of cAMP. In vitro transcription experiments demonstrated that the leu-2012 mutation created a new transcription initiation site. RNA polymerase utilized this site in vitro in the absence of added cAMP receptor protein and cAMP.

DNA supercoiling in gyrase mutants

Nucleoids isolated from Escherichia coli strains carrying temperature-sensitive gyrA or gyrB mutations were examined by sedimentation in ethidium bromide-containing sucrose density gradients. A shift to restrictive temperature resulted in nucleoid DNA relaxation in all of the mutant strains. Three of these mutants exhibited reversible nucleoid relaxation: when cultures incubated at restrictive temperature were cooled to 0 degree C over a 4- to 5-min period, supercoiling returned to levels observed with cells grown at permissive temperature. Incubation of these three mutants at restrictive temperature also caused nucleoid sedimentation rates to increase by about 50%.

DNA topoisomerase II mutant of Saccharomyces cerevisiae: topoisomerase II is required for segregation of daughter molecules at the termination of DNA replication

A temperature-sensitive DNA topoisomerase II mutant of the yeast Saccharomyces cerevisiae has been identified. Genetic analysis shows that a single recessive nuclear mutation is responsible for both temperature-sensitive growth and enzymatic activity. Thus, topoisomerase II is essential for viability and the mutation is most probably in the structural gene. Experiments with synchronized mutant cells show that at the nonpermissive temperature cells can undergo one, and only one, round of DNA replication. These cells are arrested at medial nuclear division. Analysis of 2-microns plasmid DNA from these cells shows it to be in the form of multiply intertwined catenated dimers. The results suggest that DNA topoisomerase II is necessary for the segregation of chromosomes at the termination of DNA replication.

Use of phi(glp-lac) in studies of respiratory regulation of the Escherichia coli anaerobic sn-glycerol-3-phosphate dehydrogenase genes (glpAB)

Expression of the glpA operon encoding the extrinsic membrane anaerobic sn-glycerol-3-phosphate dehydrogenase complex of Escherichia coli K-12 was studied in five strains carrying independent glpA-lac operon fusions. The location of the fusions was confirmed by transduction. Two of the strains produced an enzymatically active anaerobic sn-glycerol-3-phosphate dehydrogenase that accumulated in the cytoplasmic fraction of the cells. This suggests the loss of a specific membrane anchor subunit encoded by a distal gene, glpB, which was disrupted by the insertion. beta-Galactosidase in all five strains carrying phi(glpA-lac) was highly inducible by glycerol only anaerobically. A mutation in fnr, a pleiotropic activator gene, prevented full induction of the phi(glpA-lac), demonstrating that the Fnr protein is a positive regulator of the primary dehydrogenase as well as of the terminal reductases of anaerobic respiratory chains. Low concentrations of the respiratory poison KCN had a permissive effect on aerobic expression of phi(glpA-lac). Aerobic expression of the hybrid operon was also enhanced in isogenic derivatives of the fusion strains deficient in protoporphyrin biosynthesis (hemA). Thus, heme proteins may play a role in mediating aerobic repression of the anaerobic respiratory chain.

Plasmid-encoded regulation of colicin E1 gene expression

A plasmid-encoded factor that regulates the expression of the colicin E1 gene was found in molecular cloning experiments. The 2,294-base-pair AvaII fragment of the colicin E1 plasmid (ColE1) carrying the colicin E1 structural gene and the promoter-operator region had the same information with respect to the repressibility and inducibility of colicin E1 synthesis as the original ColE1 plasmid. An operon fusion was constructed between the 204-bp fragment containing the colicin E1 promoter-operator and xylE, the structural gene for catechol 2,3-dioxygenase encoded on the TOL plasmid of Pseudomonas putida. The synthesis of the dioxygenase from the resulting plasmid occurred in recA+, but not in recA- cells and was derepressed in the recA lexA(Def) double mutant. These results indicate that the ColE1 plasmid has no repressor gene for colicin E1 synthesis and that the lexA protein functions as a repressor. Colicin E1 gene expression was adenosine 3',5'-phosphate (cAMP) dependent. Upon the removal of two PvuII fragments (2,000 bp in length) from the ColE1 plasmid, the induced synthesis of colicin E1 occurred in the adenylate-cyclase mutant even without cAMP. The 3,100-bp Tth111I fragment of the ColE1 plasmid cloned on pACYC177 restored the cAMP dependency of the deleted ColE1 plasmid. Since the deleted fragments correspond to the mobility region of ColE1, the cAMP dependency of the gene expression should be somehow related to the plasmid mobilization function.

A type I DNA topoisomerase from Trypanosoma cruzi

A type I DNA topoisomerase has been isolated from the nuclei of the flagellate Trypanosoma cruzi, using poly(ethylene glycol) fractionation and chromatography on hydroxyapatite and on phosphocellulose. The relaxation activity was ATP-independent, enhanced by Mg2+ and spermidine. The enzyme removed supercoils from negative and positive superhelical DNAs. Topoisomerase activity was associated with a polypeptide of Mr about 65000 as shown by glycerol gradient centrifugation and by electrophoresis on sodium dodecyl sulfate/polyacrylamide gels.

Inhibition of RNA synthesis by oxolinic acid is unrelated to average DNA supercoiling

Oxolinic acid reduced RNA synthesis rates whether chromosome supercoiling decreased, increased, or remained unchanged. Thus, inhibition of RNA synthesis by oxolinic acid appears to involve factors other than average DNA supercoiling level. Coumermycin A1 caused RNA synthesis rates to increase or decrease roughly in parallel with DNA supercoiling.

Gene-protein index of Escherichia coli K-12

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Topoisomerase I from chicken erythrocytes: purification, characterization, and detection by a deoxyribonucleic acid binding assay

We have purified a deoxyribonucleic acid topoisomerase to near homogeneity from the nuclei of mature chicken erythrocytes. The enzyme relaxes supercoiled DNA in the absence of ATP or Mg2+. It is unable to resolve topologically knotted circular duplex DNA. These properties resemble those of type I eukaryotic topoisomerases capable of breaking and rejoining one strand of duplex DNA at a time. The sedimentation value of the protein is 4.4 S. The molecular weight of the reduced, denatured protein is 100K. After elution from sodium dodecyl sulfate (NaDodSO4) gels and renaturation, topoisomerase activity is found in the band at 100K and in minor bands at 95K, 78K, and 73K. The minor bands are likely to be proteolytic fragments since the Mr 100K protein is cleaved by trypsin to fragments of similar or even smaller size with retention of activity. At KCl concentrations suboptimal for the 100K form, the trypsin cleaved form is severalfold more active than the 100K form. Single-stranded DNA, but not duplex DNA or RNA, inhibits DNA relaxing activity, presumably by forming a covalent complex at the enzyme active site. Preincubation of the enzyme with single-stranded DNA leads to the depletion, in NaDodSO4-polyacrylamide gels, of protein bands corresponding to the 100K topoisomerase, its putative proteolytic fragments, and its tryptic fragments. The reaction which leads to band depletion requires active topoisomerase and conditions where single-stranded DNA inhibits relaxing activity. The band depletion technique provides a convenient assay for the polynucleotide binding activity of topoisomerases and possibly other proteins. The function of the enzyme in the inactive nuclei of mature chicken erythrocytes is unclear. The estimated content of chicken erythrocyte topoisomerase per unit DNA is comparable to that in nuclei active in replication and transcription.

Inhibition of Micrococcus luteus DNA topoisomerase I by UV photoproducts

The activity of Micrococcus luteus DNA topoisomerase I on UV-irradiated supercoiled DNA was studied under either processive or distributive reaction conditions. Changes in DNA structure caused by UV irradiation reduce the rate of DNA relaxation at very low concentration of photoproducts. Under processive conditions the inhibition of the topoisomerase I by photoproducts can be quantitated by measuring the amount of substrate left in the replicative form I band. The mode of action of DNA topoisomerase I was affected by the presence of photoproducts in the DNA substrate, although the ability of the enzyme to form a covalent complex with UV-irradiated supercoiled DNA was not changed. The inhibition of topoisomerase I by UV photoproducts has been compared to the effects of single-stranded DNA and UV-irradiated duplex linear DNA on the enzyme, and the results suggest that the inhibition by photoproducts is caused by changes in the conformation of the supercoil. Our findings indicate the possibility that DNA topoisomerase I plays a role in repair.

Cloning of the gene topA encoding for DNA topoisomerase I and the physical mapping of the cysB-topA-trp region of Escherichia coli

The gene topA of Escherichia coli that encodes for DNA topoisomerase I has been cloned by a combination of genetic and radioimmunal screening. The gene has been mapped to be within a 3.4 Kb segment of the bacterial genome. The intracellular level of the enzyme in strains harboring extrachromosomal copies of topA gene increases with increasing copy number of the gene and the introduction of extrachromosomal copies of the topA gene truncated at its 3' side into a topA strain of E. coli does not significantly influence the expression of the chromosomal copy of topA. These results suggest that the expression of topA is not tightly regulated. Strains in which DNA topoisomerase I is overproduced grow significantly slower in broth and give smaller size colonies on agar plates. Physical mapping of a 20 Kb region containing cysB; topA and trp has also been carried out with a number of restriction enzymes; topA is found to be immediately adjacent to cysB and is separated from trp by a 7 Kb segment where no known gene resides.

The lethal effect of a plasmid resulting from transcriptional readthrough of rplJ from the rplKA operon in Escherichia coli

A high-copy plasmid, pGA217, which carries a deletion (lacking the carboxy-terminal 20 amino acids) of the structural gene for ribosomal protein L10 (rplJ) is lethal to the cell in the absence of the gene (rplL) for r-proteins L7/L12, but only if the upstream operon for r-proteins L11 (rplK) and L1 (rplA) is present on the same plasmid. Measurements of beta-galactosidase activity of a hybrid protein expressed by a rplL-lacZ fusion indicated that the L10 fragment peptide which lacks the carboxy-terminal 20 amino acids is capable of exerting feedback regulation. Double transformation experiments with two compatible plasmids showed that the detrimental effect of the rplJ deletion on pGA217 can be reversed by the addition of a second plasmid which carries a functional gene for L7/L12. These two pieces of evidence suggest that the lethal effect of pGA217 is due to its property of feeding back on L7/L12 production from the chromosomal rplK gene. The upstream rplKA operon was inferred to have a cis-acting, stimulating effect on rplJ expression from the following evidence: (1) donor plasmids carrying the genes for L11 and/or L1 fail to exert a trans-acting effect, (2) deletion mutants which removed portions of rplK and/or rplA, but maintained the rplKA promoter, rplKp, still retained a severe growth-inhibiting effect. We suggest that these results can be explained by assuming that there is transcription from the rplKA promoter through rplJ and perhaps beyond.

Distribution of insertion element IS1 in natural isolates of Escherichia coli

Total DNAs from twelve natural isolates of Escherichia coli from animals and humans were examined by hybridization with a probe for IS1. Considerable variation in copy number was found. In the case of two strains isolated from the same individual, one strain contained no copies of IS1 and the other, much greater than 30. Evidence was also obtained for the existence of IS1-like elements (iso-IS1s) of greater than 15% sequence divergence relative to the IS1 from antibiotic resistance plasmid R100.

The coupled use of 'footprinting' and exonuclease III methodology for RNA polymerase binding and initiation. Application for the analysis of three tandem promoters at the control region of colicin El

In order to determine the initiation site for three promoters P1, P2 and P3 (5' to 3') in close proximity in the colicin E1 control region we developed a new methodology that couples ternary complex formation and the analysis of the 3' border protected from exonuclease III digestion. The initiation of transcription could be detected by measuring the shift in the position of the 3' protected border when RNA polymerase moved from its binary complex position to its ternary complex position. The latter stops at a specific nucleotide because transcription is initiated with one or more NTPs missing. This approach, coupled with "footprinting", can also be used to decide whether the formation of an RNA polymerase binary or ternary complex at one site excludes or weakens binding at neighboring sites. The location of 3' protected borders reveals the formation of respective binary and ternary complexes at non-saturating RNA polymerase conditions, whereas at saturating conditions only the distal 3' boundary is seen and exonuclease cannot penetrate further. However, if "footprinting" reveals proximal 5' patterns this establishes that simultaneous binding has occurred on the same DNA fragment. The data showed that this was true for P1 and P3 which are only 8 nucleotides apart. P2 could only be detected at non-saturating conditions since it overlaps both P1 and P3. The evidence from the literature and this study establishes P1 as the true colicin E1 promoter with the possibility that supercoiling may eliminate any role for P2 and P3.